Merge pull request #3 from WormBase/soba_multi

check that roots have annotations or skip, but not for soba by ontolo…

Author: raymond91125

soba_multi.cgi

@@ -1100,33 +1100,34 @@ sub annotSummaryJsonCode {
     }
 
 
-    my $pieInfo = '';
+    my $geneOnePieSize = 0;    my $geneTwoPieSize = 0;
+    my $geneOnePieOpacity = 0; my $geneTwoPieOpacity = 0;
     if ($geneOneId) {
-      my $geneOnePieSize    = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100;
-      my $geneTwoPieSize    = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100; 
+      $geneOnePieSize    = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100;
+      $geneTwoPieSize    = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100; 
       my $opacityMultiplier = 0.5;
-      my $geneOnePieOpacity = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneOne} * $opacityMultiplier;
-      my $geneTwoPieOpacity = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneTwo} * $opacityMultiplier;
-      $pieInfo = qq("geneOnePieSize" : $geneOnePieSize, "geneTwoPieSize" : $geneTwoPieSize, "geneOnePieOpacity" : $geneOnePieOpacity, "geneTwoPieOpacity" : $geneTwoPieOpacity); }
+      $geneOnePieOpacity = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneOne} * $opacityMultiplier;
+      $geneTwoPieOpacity = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneTwo} * $opacityMultiplier; }
+    my $pieInfo = qq(, "geneOnePieSize" : $geneOnePieSize, "geneTwoPieSize" : $geneTwoPieSize, "geneOnePieOpacity" : $geneOnePieOpacity, "geneTwoPieOpacity" : $geneTwoPieOpacity);
 
     my $cytId = $node; $cytId =~ s/://;
     if ($rootNodes{$node}) {
-      next unless ($nodes{$node}{'counts'}{'anygene'}{'anytype'});			# only add a root if it has annotations
+      next unless (($nodes{$node}{'counts'}{'anygene'}{'anytype'}) || ($objectsQvalue)); 	# only add a root if it has annotations or is soba by ontology terms, which don't have annoatations
       my $nodeColor  = 'blue';  if ($node eq 'GO:0000000') { $nodeColor  = '#fff'; }
       if ($goslimIds{$node}) { $backgroundColor = $nodeColor; }
 # print qq(ROOT NODE $node\n);
 #         $node =~ s/GO://; 
-        push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "$nodeColor", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidthRoot_unweighted", "borderWidthWeighted" : "$borderWidthRoot_weighted", "borderWidth" : "$borderWidthRoot", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "rectangle", "nodeExpandable" : "$nodeExpandable", $pieInfo } }); }
+        push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "$nodeColor", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidthRoot_unweighted", "borderWidthWeighted" : "$borderWidthRoot_weighted", "borderWidth" : "$borderWidthRoot", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "rectangle", "nodeExpandable" : "$nodeExpandable" $pieInfo } }); }
       elsif ($nodes{$node}{lca}) {
 # print qq(LCA NODE $node\n);
         if ($goslimIds{$node}) { $backgroundColor = 'blue'; }
 #         $node =~ s/GO://; 
-          push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "blue", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable", $pieInfo } });   }
+          push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "blue", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable" $pieInfo } });   }
       elsif ($nodes{$node}{annot}) {
 # print qq(ANNOT NODE $node\n);
          if ($goslimIds{$node}) { $backgroundColor = 'red'; }
 #          $node =~ s/GO://; 
-         push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "solid", "labelColor" : "$labelColor", "nodeColor" : "red", "annotationDirectness" : "direct", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable", $pieInfo } });     } 
+         push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "solid", "labelColor" : "$labelColor", "nodeColor" : "red", "annotationDirectness" : "direct", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable" $pieInfo } });     } 
       else {
 # print qq(OTHER NODE $node\n); 
     }